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Novel Chromosome Organization Pattern in Actinomycetales–Overlapping bioRxiv preprint doi: https://doi.org/10.1101/094169; this version posted December 14, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Novel chromosome organization pattern in actinomycetales–overlapping 2 replication cycles combined with diploidy 3 4 Kati Böhm1, Fabian Meyer1, Agata Rhomberg1, Jörn Kalinowski2, Catriona Donovan1, 5 and Marc Bramkamp1* 6 7 1Ludwig-Maximilians-Universität München, Fakultät Biologie, Großhaderner Straße 2- 8 4, 82152 Planegg-Martinsried, Germany 9 2Universität Bielefeld, Center for Biotechnology (CeBiTec), 33594 Bielefeld, Germany 10 11 Keywords: Corynebacterium, cell cylce, origin, ParB, ParA, replication, diploidy 12 13 *Corresponding author: Marc Bramkamp 14 Email: [email protected]; Phone: +49-(0)89-218074611; Fax: +49-(0)89- 15 218074621 16 17 18 1 bioRxiv preprint doi: https://doi.org/10.1101/094169; this version posted December 14, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 19 Abstract 20 21 Bacteria regulate chromosome replication and segregation tightly with cell division to 22 ensure faithful segregation of DNA to daughter generations. The underlying 23 mechanisms have been addressed in several model species. It became apparent 24 that bacteria have evolved quite different strategies to regulate DNA segregation and 25 chromosomal organization. We have investigated here how the actinobacterium 26 Corynebacterium glutamicum organizes chromosome segregation and DNA 27 replication. Unexpectedly, we find that C. glutamicum cells are at least diploid under 28 all conditions tested and that these organisms have overlapping C-periods during 29 replication with both origins initiating replication simultaneously. Based on 30 experimentally obtained data we propose growth rate dependent cell cycle models for 31 C. glutamicum. 32 33 Introduction 34 35 Bacterial chromosome organization is highly regulated, where replication coincides 36 with segregation of sister nucleoids and is tightly coordinated with cell division (1). 37 Cell cycle control mechanisms exist, which ensure constant DNA content throughout 38 cell generations. In particular, the action of the key replication initiator protein DnaA is 39 timed by various regulatory systems, for instance via the CtrA protein cascade in 40 Caulobacter crescentus or SeqA in Escherichia coli (2-6). Upon replication initiation 41 DnaA binds to the origin of replication (oriC) and mediates duplex unwinding prior to 42 loading of the replication machinery (7,8). The two evolving replication forks migrate 43 along the left and right arm of the circular chromosome towards the terminus of 2 bioRxiv preprint doi: https://doi.org/10.1101/094169; this version posted December 14, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 44 replication (terC), where FtsK-dependent XerCD recombinases resolve decatenated 45 chromosomes as a final step (9,10). Replication usually takes place within defined 46 cellular regions via stably assembled protein complexes, namely replisomes, of 47 rather static or dynamic nature (11,12). 48 The bacterial cell cycle can be divided in different stages illustrated in Figure 1. The 49 time of DNA-replication is termed C-period, which is followed by a time interval 50 necessary for cell division executed by the divisiome (D-period). Several bacteria like 51 Mycobacterium smegmatis and C. crescentus replicate their genome once within a 52 generation, where C-periods are temporally separated from each other (13,14). At 53 slow growing conditions a non-replicative state termed B-period precedes the C- 54 period (not shown), thus the bacterial cell cycle resembles in some aspects the 55 eukaryotic cell cycle (G1, S, G2 phases). Contrary to this, fast growing organisms 56 such as Bacillus subtilis, E. coli and Vibrio cholerae can overlap C-periods during fast 57 growth, a phenomenon termed multifork replication (15-17). Under these conditions a 58 new round of replication is reinitiated before termination of the previous one. 59 Therefore, generation times are considerably shorter than the duration of the C- 60 period. However, only one round of replication is initiated per cell cycle and usually 61 one C-period is completed at the time point of cell division (18). Many bacteria 62 contain only one copy of the chromosome. However, several bacteria and archaea 63 can have increased DNA contents due to oligo- or polyploidy (19). Polyploid cells 64 harbor multiple, fully replicated chromosome copies throughout their life cycle, which 65 has been frequently found in prokaryotes including certain gram-positive bacteria, 66 proteobacteria, Deinococcales, cyanobacteria and also archaea (20-27). 67 Besides the distinct cell cycle modes chromosome localization patterns differ 68 between model organisms. In a non-replicating, slow-growing E. coli cell the single 3 bioRxiv preprint doi: https://doi.org/10.1101/094169; this version posted December 14, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 69 chromosome is placed symmetrically with oriC and terC regions located at midcell 70 and the replichores spatially separated to the two cell halves (28). Upon replication 71 initiation the two sister chromosomes segregate bidirectionally to opposite cell halves 72 with replisomes positioned at midcell (29,30). Finally, oriC and terC are confined to 73 cell quarter regions. Contrary to this, the model organisms C. crescentus, Vibrio 74 cholerae and Pseudomonas aeruginosa localize their nucleoids about the 75 longitudinal axis with chromosome arms adjacent to each other (31-34). Sister 76 replichores move to the opposite cell half with the segregated oriC facing towards the 77 pole, mirroring the second chromosome at the transverse axis. The oriC region of C. 78 crescentus and V. cholera is positioned by polar landmark proteins (35,36), where 79 replisomes assemble and simultaneously move towards midcell in the course of 80 replication (12,17). For the most part, P. aeruginosa places its replication machinery 81 centrally (34). Finally, B. subtilis switches from the longitudinal chromosome 82 organization to the E. coli “left-oriC-right” configuration during replication initiation 83 (37). 84 The mitotic-like ParABS system has been identified as a driving force behind 85 coordinated nucleoid partitioning for more than two third of bacterial species 86 analyzed, with exceptions specifically within the phylum of γ-proteobacteria such as 87 E. coli (38). This segregation mechanism involves components similar to the plasmid 88 encoded par genes responsible for active segregation of low-copy-number plasmids 89 (39). Thereby, the ParB protein binds a variable number of centromere-like DNA 90 sequences called parS sites in oriC-proximity (40) and spreads along the DNA 91 forming large protein-DNA complexes (41-43). Interaction of ParB with the Walker- 92 type ATPase ParA mediates ATP-hydrolysis and thereby ParA detachment from DNA 93 (44), driving apart the sister chromosomes as the protein interaction translocates the 4 bioRxiv preprint doi: https://doi.org/10.1101/094169; this version posted December 14, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 94 oriC towards the opposite cell half (33,45,46). The precise mechanism of the 95 ParABS-mediated DNA segregation has been under debate, however, to date 96 dynamic diffusion-ratchet and DNA-relay models are favored, where nucleoid and 97 plasmid movement is mediated along a ParA gradient caused by local ParB- 98 stimulated depletion of DNA-bound ParA (47-49). Deletion of this partitioning system 99 has mild effects in B. subtilis and V. cholerae cells, but causes severe chromosome 100 segregation defects in other organisms and is essential for viability in C. crescentus 101 and Myxococcus xanthus (46,50-56). 102 Here we present the cell cycle and spatiotemporal organization of oriCs and 103 replisomes in C. glutamicum, a rod-shaped polar growing actinobacterium. It is 104 closely related to pathogens like C. diphteriae and M. tuberculosis, the latter being 105 amongst the top ten causes of fatal infections worldwide (57). Besides this, C. 106 glutamicum is of great economic importance as an amino acid and vitamin producer 107 and extensive efforts in metabolic engineering are being carried out concerning 108 metabolite production and yield increase (58). Although, its metabolism is one of the 109 best studied amongst model organisms the underlying cell cycle parameters and 110 chromosome organization patterns had so far not been analyzed in detail. C. 111 glutamicum relies on a ParABS system to segregate their nucleoids prior to cell 112 division (51,59,60). Chromosome segregation influences division site selection and, 113 hence, growth and chromosome organization are tightly coupled in C. glutamicum 114 (59). This may in part explain why protein machineries that have been described in 115 various bacterial species like the Min system or a nucleoid occlusion system, both 116 being involved in division septum placement are absent in C. glutamicum (61). 117 In this study, we tracked in vivo fluorescently labeled centromer-binding protein ParB 118 and replisome sliding clamp DnaN to investigate spatiotemporal oriC and replisome 5 bioRxiv preprint doi: https://doi.org/10.1101/094169; this version posted December 14, 2016.
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